AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i343_ecoli_mtub_100.orf -o343_ecoli_mtub_100.ace -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -g0.58 -x5 -e 
Parameter values:
 expect =  	5
 ncols =   	10
 npass =   	1000
 maxnpass =	100
 nruns =   	1000
 maxnruns =	100
 repeat =  	15
 maxreps = 	3
 nread =   	500
 ncycles = 	1
 fragment =	1
 psfact =  	0.1
 gcback =  	0.58
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	yiaY	189	putative oxidoreductase
#2	Rv0692	164	hypothetical protein Rv0692

Motif number 1

CATTTCGGCACTCGATGCCATATTGTGTCC	2	25	1	CTCGATGCCA	    0.979845	-140
AGATCGACGGATCGCTGTCGAGACCTGCTG	2	55	1	ATCGCTGTCG	    0.991925	-110
CGGTGTCGGTATCGGTTTCGTAGTCCATCT	2	99	0	ATCGGTTTCG	      0.9844	-66
CGGTGACAAGCTCGGTGTCGGTATCGGTTT	2	111	0	CTCGGTGTCG	    0.998654	-54
CAACCAGGGTCTCGGTGACAAGCTCGGTGT	2	123	0	CTCGGTGACA	    0.992385	-42
          **********

Masking position 6
Map Score:   7.57316

Number of sites scoring better than the average of aligned sites = 284
Number in coding regions = 281
Number in noncoding regions = 3
Number of orfs with sites within 600 bp upstream = 3
Fraction of orfs with sites within 600 bp upstream = 0.00048185


Motif number 2

GGCATCGAGTGCCGAAATGGAAGGGCGAAT	2	14	0	GCCGAAATGG	    0.979183	-151
ACAGCGATCCGTCGATCTGGACACAATATG	2	43	0	GTCGATCTGG	    0.996606	-122
CCTTTCGCCAGCAGGTCTCGACAGCGATCC	2	63	0	GCAGGTCTCG	    0.979678	-102
CGGTTTCGTAGTCCATCTGGATTGCCTTTC	2	87	0	GTCCATCTGG	     0.98921	-78
CAAGCTCGGTGTCGGTATCGGTTTCGTAGT	2	105	0	GTCGGTATCG	    0.990685	-60
          **********

Masking position 8
Map Score:   5.08077

Number of sites scoring better than the average of aligned sites = 868
Number in coding regions = 853
Number in noncoding regions = 15
Number of orfs with sites within 600 bp upstream = 13
Fraction of orfs with sites within 600 bp upstream = 0.00208802


Motif number 3

ATTTTAAAACTTAATTAATCATTTCC    	1	7	0	TTAATTAATC	    0.973399	-183
AGTTTTAAAATAAATTAATACAAAATTCTT	1	26	1	TAAATTAATA	    0.977845	-164
GTGCTTTTTTTAAATTCATAAGAATTTTGT	1	45	0	TAAATTCATA	    0.941652	-145
AGCACATTGTTTAATGAATACAATGTGCTT	1	70	1	TTAATGAATA	    0.952115	-120
ATTGATTATCAAAATTAATCTAATAAAAAG	1	97	0	AAAATTAATC	    0.951485	-93
ATTAATTTTGATAATCAATAATACTGATCA	1	108	1	ATAATCAATA	    0.914213	-82
          **********

Masking position 5
Map Score:   4.84786

Number of sites scoring better than the average of aligned sites = 108
Number in coding regions = 56
Number in noncoding regions = 52
Number of orfs with sites within 600 bp upstream = 57
Fraction of orfs with sites within 600 bp upstream = 0.00915516


Motif number 4

ATAAATTAATACAAAATTCTTATGAATTTA	1	35	1	ACAAAATTCT	    0.862878	-155
TATTCATTAAACAATGTGCTTTTTTTAAAT	1	60	0	ACAATGTGCT	    0.992056	-130
TTTAATGAATACAATGTGCTTTTTATTAGA	1	79	1	ACAATGTGCT	    0.992056	-111
TTTTCATTCGAAAATATGATCAGTATTATT	1	124	0	AAAATATGAT	    0.880192	-66
CGATCTGGACACAATATGGCATCGAGTGCC	2	31	0	ACAATATGGC	    0.929312	-134
          **********

Masking position 4
Map Score:   3.02168

Number of sites scoring better than the average of aligned sites = 209
Number in coding regions = 183
Number in noncoding regions = 26
Number of orfs with sites within 600 bp upstream = 30
Fraction of orfs with sites within 600 bp upstream = 0.0048185


Motif number 5

TTTAAATTCATAAGAATTTTGTATTAATTT	1	37	0	TAAGAATTTT	    0.854532	-153
CATTAAACAATGTGCTTTTTTTAAATTCAT	1	56	0	TGTGCTTTTT	    0.983423	-134
ATGAATACAATGTGCTTTTTATTAGATTAA	1	83	1	TGTGCTTTTT	    0.983423	-107
TCAATAATACTGATCATATTTTCGAATGAA	1	122	1	TGATCATATT	    0.876456	-68
GGCAGCTTACTGAGGATTTTCATTCGAAAA	1	140	0	TGAGGATTTT	    0.978466	-50
          **********

Masking position 7
Map Score:   1.70129

Number of sites scoring better than the average of aligned sites = 614
Number in coding regions = 519
Number in noncoding regions = 95
Number of orfs with sites within 600 bp upstream = 107
Fraction of orfs with sites within 600 bp upstream = 0.017186


Motif number 6

TAATACAAAATTCTTATGAATTTAAAAAAA	1	41	1	TTCTTATGAA	    0.809257	-149
ATCAAAATTAATCTAATAAAAAGCACATTG	1	90	0	ATCTAATAAA	    0.860943	-100
TGATCATATTTTCGAATGAAAATCCTCAGT	1	132	1	TTCGAATGAA	    0.972919	-58
TTGTGTCCAGATCGACGGATCGCTGTCGAG	2	47	1	ATCGACGGAT	    0.961889	-118
AGAGGTGTCCATCGACGGAAT         	2	154	1	ATCGACGGAA	    0.987784	-11
          **********

Masking position 2
Map Score:   0.831716

Number of sites scoring better than the average of aligned sites = 311
Number in coding regions = 265
Number in noncoding regions = 46
Number of orfs with sites within 600 bp upstream = 61
Fraction of orfs with sites within 600 bp upstream = 0.00979762


Motif number 7

          **********

No masking
Map Score:   -3.31523e-13

Number of sites scoring better than the average of aligned sites = 0
Number in coding regions = 0
Number in noncoding regions = 0
Number of orfs with sites within 600 bp upstream = 0
Fraction of orfs with sites within 600 bp upstream = 0


Motif number 8

          **********

No masking
Map Score:   -3.31523e-13

Number of sites scoring better than the average of aligned sites = 0
Number in coding regions = 0
Number in noncoding regions = 0
Number of orfs with sites within 600 bp upstream = 0
Fraction of orfs with sites within 600 bp upstream = 0


Motif number 9

          **********

No masking
Map Score:   -3.31523e-13

Number of sites scoring better than the average of aligned sites = 0
Number in coding regions = 0
Number in noncoding regions = 0
Number of orfs with sites within 600 bp upstream = 0
Fraction of orfs with sites within 600 bp upstream = 0